Lintr cleanup in tests

.lintr

@@ -1,5 +1,4 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
-  cyclocomp_linter = NULL,
   object_usage_linter = NULL
   )

design/design_signature_module.Rmd

@@ -16,11 +16,11 @@ library(checkmate)
 
 ## Objectives
 
-We need a shiny module that captures the gene signature logic. We might also need additional functions and classes which capture reused functionality. 
+We need a shiny module that captures the gene signature logic. We might also need additional functions and classes which capture reused functionality.
 
 ## Hermes Interface
 
-### Helpers 
+### Helpers
 
 ```{r}
 shorten_list <- function(x) {

tests/testthat/test-adtteSpec.R

@@ -178,8 +178,6 @@ test_that("adtteSpecInput creates expected HTML", {
   expect_class(result, "shiny.tag")
 })
 
-# nolint start
-
 test_that("adtteSpecServer module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -242,5 +240,3 @@ test_that("adtteSpecServer module works as expected in the test app", {
   app$click(ns_fp("ADTTE-filter-ADTTE_PARAMCD-remove"))
   app$stop()
 })
-
-# nolint end

tests/testthat/test-assaySpec.R

@@ -9,8 +9,6 @@ test_that("assaySpecInput creates expected HTML", {
   expect_class(result, "shiny.tag")
 })
 
-# nolint start
-
 # assaySpecServer ----
 test_that("assaySpecServer module works as expected in the test app", {
   skip_if_covr()
@@ -54,5 +52,3 @@ test_that("assaySpecServer module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end

tests/testthat/test-barplot.R

@@ -19,8 +19,6 @@ test_that("ui_g_barplot creates expected HTML", {
 
 # tm_g_barplot ----
 
-# nolint start
-
 test_that("barplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -97,5 +95,3 @@ test_that("barplot module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end

tests/testthat/test-boxplot.R

@@ -15,8 +15,6 @@ test_that("ui_g_boxplot creates expected HTML", {
 
 # tm_g_boxplot ----
 
-# nolint start
-
 test_that("boxplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -64,5 +62,3 @@ test_that("boxplot module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end

tests/testthat/test-experimentSpec.R

@@ -89,8 +89,6 @@ test_that("h_gene_data does not fail when object does not contain any genes", {
   expect_identical(result, expected)
 })
 
-# nolint start
-
 test_that("experimentSpec module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -170,5 +168,3 @@ test_that("experimentSpec module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end

tests/testthat/test-forest.R

@@ -19,8 +19,6 @@ test_that("ui_g_forest_tte creates expected HTML", {
 
 # tm_g_forest_tte ----
 
-# nolint start
-
 test_that("forest_tte module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -68,5 +66,3 @@ test_that("forest_tte module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end

tests/testthat/test-geneSpec.R

@@ -32,8 +32,6 @@ test_that("h_parse_genes correctly returns empty data frame when no genes match"
 
 # geneSpecServer ----
 
-# nolint start
-
 test_that("geneSpec module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -80,7 +78,10 @@ test_that("geneSpec module works as expected in the test app", {
   ns_fp <- active_module_filter_panel_ns(app)
   app$set_inputs(!!ns_fp("MAE-MAE-hd1-row_to_add") := "chromosome", allow_no_input_binding_ = TRUE)
   app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection") := c("1", "2"))
-  app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
+  app$set_inputs(
+    !!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE,
+    allow_no_input_binding_ = TRUE
+  )
   app$wait_for_idle()
 
   # Confirm that gene selection was not changed.
@@ -122,5 +123,3 @@ test_that("geneSpec module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end

tests/testthat/test-km.R

@@ -20,8 +20,6 @@ test_that("ui_g_km creates expected HTML", {
 
 # tm_g_km ----
 
-# nolint start
-
 test_that("km module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -66,5 +64,3 @@ test_that("km module works as expected in the test app", {
   )
   app$stop()
 })
-
-# nolint end

tests/testthat/test-pca.R

@@ -14,8 +14,6 @@ test_that("ui_g_pca creates HTML", {
 
 # pca Server ----
 
-# nolint start
-
 test_that("pca module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -65,7 +63,10 @@ test_that("pca module works as expected in the test app", {
   ns_fp <- active_module_filter_panel_ns(app)
   app$set_inputs(!!ns_fp("MAE-MAE-hd1-row_to_add") := "chromosome", allow_no_input_binding_ = TRUE)
   app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection") := character())
-  app$set_inputs(!!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
+  app$set_inputs(
+    !!ns_fp("MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE,
+    allow_no_input_binding_ = TRUE
+  )
   app$wait_for_idle()
 
   res <- app$get_value(output = ns("test_pca"))
@@ -231,5 +232,3 @@ test_that("pca module works as expected in the test app", {
   expect_identical(res, 2500L)
   app$stop()
 })
-
-# nolint end

tests/testthat/test-quality.R

@@ -16,8 +16,6 @@ test_that("ui_g_quality creates expected HTML", {
 
 # tm_g_quality ----
 
-# nolint start
-
 test_that("quality module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -81,5 +79,3 @@ test_that("quality module works as expected in the test app", {
   )
   app$stop()
 })
-
-# nolint end

tests/testthat/test-sampleVarSpec.R

@@ -166,8 +166,6 @@ test_that("sampleVarSpecServer only gives factor columns in col_data_vars when c
   )
 })
 
-# nolint start
-
 test_that("sampleVarSpec module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -224,5 +222,3 @@ test_that("sampleVarSpec module works as expected in the test app", {
   expect_match(res, "< 18/>= 18 \n         5 ")
   app$stop()
 })
-
-# nolint end

tests/testthat/test-scatterplot.R

@@ -19,8 +19,6 @@ test_that("ui_g_scatterplot creates expected HTML", {
 
 # tm_g_scatterplot ----
 
-# nolint start
-
 test_that("scatterplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -102,5 +100,3 @@ test_that("scatterplot module works as expected in the test app", {
 
   app$stop()
 })
-
-# nolint end

tests/testthat/test-volcanoplot.R

@@ -14,8 +14,6 @@ test_that("ui_g_volcanoplot creates expected HTML", {
 
 # tm_g_volcanoplot ----
 
-# nolint start
-
 test_that("volcanoplot module works as expected in the test app", {
   skip_if_covr()
   skip_if_too_deep(5)
@@ -57,5 +55,3 @@ test_that("volcanoplot module works as expected in the test app", {
   expect_snapshot(cat(res))
   app$stop()
 })
-
-# nolint end